Purpose The aim of this study was to compare the level of metal contamination in two bays in the middle part of the Eastern Adriatic coastal zone in Croatia using the gills of mussels Mytilus galloprovincialis as indicator tissue. Despite the existing sources of contamination, previous studies with caged mussels only indicated moderate metal contamination of the Kaštela Bay, contrary to the Trogir Bay in which marina and shipyard present a probable source of Cu- and Zn-contamination. Methods The measurements of metallothioneins (MTs) and metals that induce MT synthesis (Cu, Zn, and Cd) were performed in the heat-treated gill cytosol and total proteins (TPs) in the untreated gill cytosol. MTs were determined by differential pulse voltammetry, Cu and Zn by flame atomic absorption spectrometry (AAS), Cd by graphite furnace AAS, and TPs by Bradford spectrophotometric procedure. Results The results collected in four sampling campaigns (autumn periods from 2001 to 2004) indicated that MT levels in mussel gills (expressed on dry mass basis 2.3 ± 0.3 mg g⁻¹) were comparable with basal levels reported in the literature (2.5 ± 0.8 mg g⁻¹). Observed interindividual, temporal, and spatial MT variability could be associated with different confounding factors, such as the time of sampling, total protein concentration, and mussel size rather than cytosolic levels of Cu and Zn. Metal levels, expressed on wet mass basis, in the heat-treated gill cytosol ranged from 1.33 to 11.31 μg g⁻¹ for Zn, from 0.72 to 2.96 μg g⁻¹ for Cu, and from 0.036 to 0.100 μg g⁻¹ for Cd. The highest Zn level was measured at Vranjic (Kaštela Bay)—the site influenced by untreated domestic wastewater, while somewhat increased Zn and the highest Cu levels were found at marina and shipyard locations (Trogir Bay). The highest Cd level was measured at Inavinil (Kaštela Bay). Conclusions The observed association of gill MT levels with several biotic and abiotic factors limits its use as the biomarker of low-level metal exposure. Therefore, the use of the metal concentrations in the heat-treated gill cytosol of Mediterranean mussels should be considered for the assessment of the low-level metal contamination of coastal marine areas.